import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
+import jalview.gui.JvSummaryTable;
import jalview.gui.JvSwingUtils;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.CardLayout;
+import java.awt.Component;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.GridLayout;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Map;
import javax.swing.ImageIcon;
import javax.swing.JButton;
import javax.swing.JFrame;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
+import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
+import javax.swing.JSeparator;
import javax.swing.JTabbedPane;
import javax.swing.JTable;
import javax.swing.JTextField;
+import javax.swing.ListCellRenderer;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.event.DocumentEvent;
import javax.swing.event.DocumentListener;
+import javax.swing.event.InternalFrameEvent;
@SuppressWarnings("serial")
/**
protected JButton btn_pdbFromFile = new JButton();
+ protected JButton btn_runPhyre2Prediction = new JButton();
+
protected JTextField txt_search = new JTextField(14);
private JPanel pnl_actions = new JPanel();
private JPanel pnl_fileChooser = new JPanel(new FlowLayout());
+ private JPanel pnl_phyre2Prediction = new JPanel(new FlowLayout());
+
+ private JPanel pnl_phyre2PredictionBL = new JPanel(new BorderLayout());
+
private JPanel pnl_idInputBL = new JPanel(new BorderLayout());
private JPanel pnl_fileChooserBL = new JPanel(new BorderLayout());
protected JLabel lbl_fromFileStatus = new JLabel(errorImage);
+ protected AssciateSeqPanel phyre2InputAssSeqPanel = new AssciateSeqPanel();
+
protected AssciateSeqPanel idInputAssSeqPanel = new AssciateSeqPanel();
protected AssciateSeqPanel fileChooserAssSeqPanel = new AssciateSeqPanel();
protected static final String VIEWS_LOCAL_PDB = "VIEWS_LOCAL_PDB";
- protected JTable tbl_summary = new JTable()
- {
- @Override
- public String getToolTipText(MouseEvent evt)
- {
- String toolTipText = null;
- java.awt.Point pnt = evt.getPoint();
- int rowIndex = rowAtPoint(pnt);
- int colIndex = columnAtPoint(pnt);
-
- try
- {
- if (getValueAt(rowIndex, colIndex) == null)
- {
- return null;
- }
- toolTipText = getValueAt(rowIndex, colIndex).toString();
- } catch (Exception e)
- {
- // e.printStackTrace();
- }
- toolTipText = (toolTipText == null ? null
- : (toolTipText.length() > 500 ? JvSwingUtils.wrapTooltip(
- true, "\"" + toolTipText.subSequence(0, 500)
- + "...\"") : JvSwingUtils.wrapTooltip(true,
- toolTipText)));
- return toolTipText;
- }
- };
-
- protected JScrollPane scrl_foundStructures = new JScrollPane(tbl_summary);
+ protected static final String VIEWS_PHYRE2_PREDICTION = "VIEWS_PHYRE2_PREDICTION";
protected JTable tbl_local_pdb = new JTable();
protected JScrollPane scrl_localPDB = new JScrollPane(tbl_local_pdb);
- private JTabbedPane pnl_filter = new JTabbedPane();
+ protected JTabbedPane pnl_filter = new JTabbedPane();
- private FTSDataColumnPreferences pdbDocFieldPrefs = new FTSDataColumnPreferences(
- PreferenceSource.STRUCTURE_CHOOSER, PDBFTSRestClient.getInstance());
+ protected FTSDataColumnPreferences pdbDocFieldPrefs = new FTSDataColumnPreferences(
+ PreferenceSource.STRUCTURE_CHOOSER,
+ PDBFTSRestClient.getInstance());
protected FTSDataColumnI[] previousWantedFields;
+ protected static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
+
+ private JTable tbl_summary = new JvSummaryTable(tempUserPrefs);
+
+
+ protected JScrollPane scrl_foundStructures = new JScrollPane(tbl_summary);
+
+ JPanel phyreResultPanel = new JPanel(new BorderLayout());
+
+ protected static Map<String, Integer> tempPrefsForPhyre = new HashMap<String, Integer>();
+
+ private JTable tbl_phyre2_summary = new JvSummaryTable(tempPrefsForPhyre);
+
+ protected JScrollPane scrl_phyre2Summary = new JScrollPane(
+ tbl_phyre2_summary);
+
public GStructureChooser()
{
try
*
* @throws Exception
*/
+ @SuppressWarnings("unchecked")
private void jbInit() throws Exception
{
+ Integer width = tempUserPrefs.get("structureChooser.width") == null ? 800
+ : tempUserPrefs.get("structureChooser.width");
+ Integer height = tempUserPrefs.get("structureChooser.height") == null ? 400
+ : tempUserPrefs.get("structureChooser.height");
tbl_summary.setAutoCreateRowSorter(true);
tbl_summary.getTableHeader().setReorderingAllowed(false);
tbl_summary.addMouseListener(new MouseAdapter()
}
}
evt.consume();
+ break;
default:
return;
}
@Override
public void actionPerformed(ActionEvent e)
{
- mainFrame.dispose();
+ closeAction(pnl_filter.getHeight());
}
});
btn_cancel.addKeyListener(new KeyAdapter()
{
if (evt.getKeyCode() == KeyEvent.VK_ENTER)
{
- mainFrame.dispose();
+ closeAction(pnl_filter.getHeight());
}
}
});
}
});
- scrl_foundStructures.setPreferredSize(new Dimension(500, 300));
- scrl_foundStructures
- .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+ btn_pdbFromFile.setFont(new java.awt.Font("Verdana", 0, 12));
+ tbl_phyre2_summary.setAutoCreateRowSorter(true);
+ tbl_phyre2_summary.getTableHeader().setReorderingAllowed(false);
+
+ tbl_phyre2_summary.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ validateSelections();
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent e)
+ {
+ validateSelections();
+ }
+ });
+ tbl_phyre2_summary.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ validateSelections();
+ switch (evt.getKeyCode())
+ {
+ case KeyEvent.VK_ESCAPE: // escape key
+ mainFrame.dispose();
+ break;
+ case KeyEvent.VK_ENTER: // enter key
+ if (btn_view.isEnabled())
+ {
+ ok_ActionPerformed();
+ }
+ break;
+ case KeyEvent.VK_TAB: // tab key
+ if (evt.isShiftDown())
+ {
+ cmb_filterOption.requestFocus();
+ }
+ else
+ {
+ if (btn_view.isEnabled())
+ {
+ btn_view.requestFocus();
+ }
+ else
+ {
+ btn_cancel.requestFocus();
+ }
+ }
+ evt.consume();
+ break;
+ default:
+ return;
+ }
+ }
+ });
+
+ String btn_runPhyre2Prediction_title = MessageManager
+ .getString("label.run_phyre2_prediction");
+ btn_runPhyre2Prediction
+ .setText(btn_runPhyre2Prediction_title + " ");
+ btn_runPhyre2Prediction
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ predict3DModelWithPhyre2();
+ }
+ });
+ btn_runPhyre2Prediction.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ if (evt.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ predict3DModelWithPhyre2();
+ }
+ }
+ });
- scrl_localPDB.setPreferredSize(new Dimension(500, 300));
+ scrl_foundStructures.setPreferredSize(new Dimension(width, height));
+
+ scrl_localPDB.setPreferredSize(new Dimension(width, height));
scrl_localPDB
.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
chk_invertFilter.setFont(new java.awt.Font("Verdana", 0, 12));
chk_rememberSettings.setFont(new java.awt.Font("Verdana", 0, 12));
chk_rememberSettings.setVisible(false);
-
- txt_search.setToolTipText(MessageManager
- .getString("label.enter_pdb_id"));
+ txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.enter_pdb_id")));
cmb_filterOption.setToolTipText(MessageManager
.getString("info.select_filter_option"));
txt_search.getDocument().addDocumentListener(new DocumentListener()
});
cmb_filterOption.addItemListener(this);
+
+ // add CustomComboSeparatorsRenderer to filter option combo-box
+ cmb_filterOption.setRenderer(new CustomComboSeparatorsRenderer(
+ (ListCellRenderer<Object>) cmb_filterOption.getRenderer())
+ {
+ @Override
+ protected boolean addSeparatorAfter(JList list, FilterOption value,
+ int index)
+ {
+ return value.isAddSeparatorAfter();
+ }
+ });
+
chk_invertFilter.addItemListener(this);
pnl_actions.add(chk_rememberSettings);
pnl_fileChooserBL.add(fileChooserAssSeqPanel, BorderLayout.NORTH);
pnl_fileChooserBL.add(pnl_fileChooser, BorderLayout.CENTER);
+ scrl_phyre2Summary.setPreferredSize(new Dimension(width, height));
+ scrl_phyre2Summary
+ .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+
+ phyreResultPanel.add(pnl_phyre2Prediction, BorderLayout.NORTH);
+ phyreResultPanel.add(scrl_phyre2Summary, BorderLayout.CENTER);
+
+ pnl_phyre2Prediction.add(btn_runPhyre2Prediction);
+ pnl_phyre2PredictionBL.add(phyre2InputAssSeqPanel, BorderLayout.NORTH);
+ pnl_phyre2PredictionBL.add(phyreResultPanel, BorderLayout.CENTER);
+
pnl_idInput.add(txt_search);
pnl_idInput.add(lbl_pdbManualFetchStatus);
pnl_idInputBL.add(idInputAssSeqPanel, BorderLayout.NORTH);
btn_cancel.setEnabled(false);
btn_view.setVisible(false);
btn_cancel.setVisible(false);
- previousWantedFields = FTSDataColumnPreferences
+ previousWantedFields = pdbDocFieldPrefs
.getStructureSummaryFields().toArray(
new FTSDataColumnI[0]);
}
}
};
pnl_filter.addChangeListener(changeListener);
- pnl_filter.setPreferredSize(new Dimension(500, 300));
+ pnl_filter.setPreferredSize(new Dimension(width, height));
pnl_filter.add(foundStructureSummary, scrl_foundStructures);
pnl_filter.add(configureCols, pdbDocFieldPrefs);
pnl_switchableViews.add(pnl_idInputBL, VIEWS_ENTER_ID);
pnl_switchableViews.add(pnl_filter, VIEWS_FILTER);
pnl_switchableViews.add(pnl_locPDB, VIEWS_LOCAL_PDB);
+ pnl_switchableViews
+ .add(pnl_phyre2PredictionBL, VIEWS_PHYRE2_PREDICTION);
this.setLayout(mainLayout);
this.add(pnl_main, java.awt.BorderLayout.NORTH);
statusPanel.add(statusBar, null);
this.add(pnl_actionsAndStatus, java.awt.BorderLayout.SOUTH);
+ mainFrame
+ .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosing(InternalFrameEvent e)
+ {
+ closeAction(pnl_filter.getHeight());
+ }
+ });
mainFrame.setVisible(true);
mainFrame.setContentPane(this);
mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
- Desktop.addInternalFrame(mainFrame, frameTitle, 800, 400);
+ Integer x = tempUserPrefs.get("structureChooser.x");
+ Integer y = tempUserPrefs.get("structureChooser.y");
+ if (x != null && y != null)
+ {
+ mainFrame.setLocation(x, y);
+ }
+ Desktop.addInternalFrame(mainFrame, frameTitle, width, height);
+ }
+
+ protected void closeAction(int preferredHeight)
+ {
+ tempUserPrefs.put("structureChooser.width", pnl_filter.getWidth());
+ tempUserPrefs.put("structureChooser.height",
+ pnl_filter.getHeight() - 76);
+ tempUserPrefs.put("structureChooser.x", mainFrame.getX());
+ tempUserPrefs.put("structureChooser.y", mainFrame.getY());
+ mainFrame.dispose();
}
public boolean wantedFieldsUpdated()
return true;
}
- return Arrays.equals(FTSDataColumnPreferences.getStructureSummaryFields()
- .toArray(new FTSDataColumnI[0]),
- previousWantedFields) ? false : true;
+ FTSDataColumnI[] currentWantedFields = pdbDocFieldPrefs
+ .getStructureSummaryFields().toArray(new FTSDataColumnI[0]);
+ return Arrays.equals(currentWantedFields, previousWantedFields) ? false
+ : true;
}
private String view;
- public FilterOption(String name, String value, String view)
+ private boolean addSeparatorAfter;
+
+ public FilterOption(String name, String value, String view,
+ boolean addSeparatorAfter)
{
this.name = name;
this.value = value;
this.view = view;
+ this.addSeparatorAfter = addSeparatorAfter;
}
public String getName()
{
return this.name;
}
+
+ public boolean isAddSeparatorAfter()
+ {
+ return addSeparatorAfter;
+ }
+
+ public void setAddSeparatorAfter(boolean addSeparatorAfter)
+ {
+ this.addSeparatorAfter = addSeparatorAfter;
+ }
}
/**
}
}
+ public JTable getResultTable()
+ {
+ return tbl_summary;
+ }
+
public JComboBox<FilterOption> getCmbFilterOption()
{
return cmb_filterOption;
}
- protected abstract void stateChanged(ItemEvent e);
- protected abstract void updateCurrentView();
+ public JTable getPhyreResultTable()
+ {
+ return tbl_phyre2_summary;
+ }
- protected abstract void populateFilterComboBox();
+ public abstract class CustomComboSeparatorsRenderer implements
+ ListCellRenderer<Object>
+ {
+ private ListCellRenderer<Object> regent;
+
+ private JPanel separatorPanel = new JPanel(new BorderLayout());
+
+ private JSeparator jSeparator = new JSeparator();
+
+ public CustomComboSeparatorsRenderer(ListCellRenderer<Object> listCellRenderer)
+ {
+ this.regent = listCellRenderer;
+ }
+
+ @Override
+ public Component getListCellRendererComponent(JList list,
+ Object value,
+ int index, boolean isSelected, boolean cellHasFocus)
+ {
+
+ Component comp = regent.getListCellRendererComponent(list, value,
+ index, isSelected, cellHasFocus);
+ if (index != -1
+ && addSeparatorAfter(list, (FilterOption) value, index))
+ {
+ separatorPanel.removeAll();
+ separatorPanel.add(comp, BorderLayout.CENTER);
+ separatorPanel.add(jSeparator, BorderLayout.SOUTH);
+ return separatorPanel;
+ }
+ else
+ {
+ return comp;
+ }
+ }
+
+ protected abstract boolean addSeparatorAfter(JList list,
+ FilterOption value,
+ int index);
+ }
+
+ protected abstract void stateChanged(ItemEvent e);
protected abstract void ok_ActionPerformed();
public abstract void tabRefresh();
public abstract void validateSelections();
-}
+
+ public abstract void predict3DModelWithPhyre2();
+
+}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff